removed noise cov & results perm only

I removed the extra noise from the covariance calculation, and created a
function Cov.suped (instead of randCov.suped).  Therefore,
sim.setup.noise.suped needed to be updated.  While I was updating the
simulation function, I removed all of the library & sourcing junk.

Additionally, I changed the output to be based on the permutation curve
only.